Download opal zip file :
You must have Java version ≥ 5
for Opal versions 0.9.x and up (Java ≥ 1.4 for earlier Opal versions).
Read the documentation page for further instructions.
You may also download the
Current Stable Version
Latest Beta Version
- Recompiled 2.1.2 to run with Java 1.5 or 1.6. Previously only ran on 1.7
The development version of Opal v3 can be found at Github (http://git.io/Opal).
- Added support for Adaptive Local Realignment (see the Facet website)
- Added documentation for adaptive local realignment and parameter advising
Previous Versions (placed here for the sake of posterity; no reason to use them)
- Added the ability of run multiple alignments with different configurations in parallel
- Added Facet estimator, which can be calculated when given predicted structure
- Allows for advising using Facet (parameter advising sets can be found on the Facet website)
- Allows user to specify replacement matrix other then BLOSUM62, either one one several built in matrices or as file input.
- Fixed shell script to work on OS X (and BSD)
- Fixed error mode raised by alignments of a very large number of sequences due
to number overflow (identified by Nam Nguyen)
- Missing source code for some modules, now added to tgz file
- Missing 00README file added to .tgz file
- added --mem flag to shell script
- Slight memory reduction in multiple alignment
- Added a shell script that runs Opal.jar with appropriate Java flags
- Bundled in a .tgz file
- Enabled methods for incorporating predicted protein secondary structure,
including development of a script to control psipred
Fixes error when guide tree is provided. Previous version would iterate, building a new tree (and crash along the way).
Correctly handles windows newline characters in fasta files.
Reduced peak memory consumption by roughly 40%.
The first official release, coincident with it's release
Several interface and logging changes to accomodate inclusion in Mesquite.
Includes support for nucleotide sequences
Opal was originally implemented as a C program (Why switch to Java? Read this).
Download opal as a zipped or tar/gzipped archive:
To unpackage the files, run
gzip -dc opal_0.2.0.tar.gz | tar -xvf -
To compile and run opal, do the following:
./Opal -f your_file